Roland, I'm not quite sure that I follow exactly what you are proposing,
but you may be interested in our recent preprint on handling inapplicable

This solution to inapplicable data is implemented in the R package
TreeSearch.  I'm still working on making this package easier to use so
would be interested to hear whether you find it useful.




*Martin R. Smith*
Assistant Professor in Palaeontology
Department of Earth Sciences
Durham University
Mountjoy Site, South Road
Durham DH1 3LE

*T*: +44 191 334 2320
*M*: +44 774 353 7510
*Skype*: martin--smith

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> Message: 1
> Date: Thu, 8 Feb 2018 17:27:54 +0100
> From: Roland Sookias <>
> To:
> Subject: [R-sig-phylo] Not inferring homology within "absence" state
>         in phylogenetic analysis
> Message-ID:
>         <CA+PBJbmF2-_VE=4HuXZ610kh_Dtm2i4hK7CZkcfza2yN=1UrOg@
> Content-Type: text/plain; charset="utf-8"
>  Dear all
> Maybe someone has some insight here...
> I am coming up against the problem, when it comes to phylogenetic analysis.
> Basically I want to conduct a parsimony (or other phylogenetic) analysis
> where "inapplicable" scores are treated as separate states *for each taxon*
> .
> I.e. I want to hypothesize shared ancestry for taxa scored with one state
> (let's say state 0), but not hypothesize shared ancestry for the other
> taxa. However, I still want to penalize a change in state from and to state
> 0.
> There are three approaches which I have thought about, but none seems to
> fit the bill:
> -Score all taxa not showing state 0 as separate states. This should do what
> I want, but the problem here is the limit on the number of states in most
> programmes.
> -Scoring binary presence/absence. The problem is here that it could end up
> being parsimonious to group the "absence" state together, when there is no
> reason to infer homology within (i.e. for taxa scored with) this state.
> -Score as 0 and inapplicable. The problem is this does not penalize a
> change from 0 to inapplicable.
> A real life example, is the shape of the ilium in crocodiles. I want to say
> that it is likely that a particular curve in the dorsal margin of the ilium
> in crocodile-line crocodilians is homologous, but I don't want to
> hypothesize homology of those taxa "lacking" this state. They are all
> equally far from each other.
> Thanks very much indeed
> Best
> Roland Sookias
>         [[alternative HTML version deleted]]

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